For vias, you can just solder a wire through on both sides. HOLES that need to connect top and bottom AND accept a component lead are another matter, and are a real pain on homebrew boards. I've been known to put extra vias immediately next to such pins, so that I can stick a wire through the via (not too hard) and not worry about having to solder both sides of the component pin (sometimes impossible) or using rivets or the equiv. Of course this only works if you're designing the board yourself, rather than using a published design.